[2024-01-24 11:05:27,774] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:27,776] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:27,777] [INFO] DQC Reference Directory: /var/lib/cwl/stg20db37fe-baf0-42fb-91d6-352366548dc7/dqc_reference
[2024-01-24 11:05:29,180] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:29,181] [INFO] Task started: Prodigal
[2024-01-24 11:05:29,181] [INFO] Running command: gunzip -c /var/lib/cwl/stg483030e0-8d91-4612-80d5-917563f59259/GCF_014634805.1_ASM1463480v1_genomic.fna.gz | prodigal -d GCF_014634805.1_ASM1463480v1_genomic.fna/cds.fna -a GCF_014634805.1_ASM1463480v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:33,569] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:33,569] [INFO] Task started: HMMsearch
[2024-01-24 11:05:33,569] [INFO] Running command: hmmsearch --tblout GCF_014634805.1_ASM1463480v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20db37fe-baf0-42fb-91d6-352366548dc7/dqc_reference/reference_markers.hmm GCF_014634805.1_ASM1463480v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:33,821] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:33,822] [INFO] Found 6/6 markers.
[2024-01-24 11:05:33,842] [INFO] Query marker FASTA was written to GCF_014634805.1_ASM1463480v1_genomic.fna/markers.fasta
[2024-01-24 11:05:33,842] [INFO] Task started: Blastn
[2024-01-24 11:05:33,843] [INFO] Running command: blastn -query GCF_014634805.1_ASM1463480v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20db37fe-baf0-42fb-91d6-352366548dc7/dqc_reference/reference_markers.fasta -out GCF_014634805.1_ASM1463480v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:34,459] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:34,462] [INFO] Selected 15 target genomes.
[2024-01-24 11:05:34,462] [INFO] Target genome list was writen to GCF_014634805.1_ASM1463480v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:34,468] [INFO] Task started: fastANI
[2024-01-24 11:05:34,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg483030e0-8d91-4612-80d5-917563f59259/GCF_014634805.1_ASM1463480v1_genomic.fna.gz --refList GCF_014634805.1_ASM1463480v1_genomic.fna/target_genomes.txt --output GCF_014634805.1_ASM1463480v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:41,008] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:41,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20db37fe-baf0-42fb-91d6-352366548dc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:41,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20db37fe-baf0-42fb-91d6-352366548dc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:41,020] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:41,020] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:41,020] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Leuconostoc falkenbergense	strain=LMG 10779	GCA_014634805.1	2766470	2766470	type	True	100.0	604	607	95	conclusive
Leuconostoc pseudomesenteroides	strain=NCDO 768	GCA_012396745.1	33968	33968	suspected-type	True	92.6169	519	607	95	below_threshold
Leuconostoc pseudomesenteroides	strain=FDAARGOS_1003	GCA_016127255.1	33968	33968	suspected-type	True	92.5358	509	607	95	below_threshold
Leuconostoc pseudomesenteroides	strain=LMG 11482	GCA_014634745.1	33968	33968	suspected-type	True	92.488	521	607	95	below_threshold
Leuconostoc mesenteroides subsp. jonggajibkimchii	strain=DRC1506	GCA_001886915.1	2026657	1245	type	True	80.5971	201	607	95	below_threshold
Leuconostoc mesenteroides subsp. mesenteroides	strain=NBRC 100496	GCA_007990165.1	33967	1245	type	True	80.5644	213	607	95	below_threshold
Leuconostoc kimchii	strain=IMSNU 11154	GCA_000092505.1	136609	136609	type	True	79.8764	195	607	95	below_threshold
Leuconostoc gelidum subsp. gelidum	strain=KCTC 3527	GCA_000166715.2	1607839	1244	type	True	79.6074	147	607	95	below_threshold
Leuconostoc rapi	strain=DSM 27776	GCA_016908715.1	1406906	1406906	type	True	79.1689	160	607	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=NBRC 113245	GCA_019655955.1	115778	1244	type	True	79.1282	157	607	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=type strain: LMG 18811	GCA_000196855.1	115778	1244	type	True	78.9917	156	607	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:41,022] [INFO] DFAST Taxonomy check result was written to GCF_014634805.1_ASM1463480v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:41,023] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:41,023] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:41,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20db37fe-baf0-42fb-91d6-352366548dc7/dqc_reference/checkm_data
[2024-01-24 11:05:41,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:41,049] [INFO] Task started: CheckM
[2024-01-24 11:05:41,049] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014634805.1_ASM1463480v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014634805.1_ASM1463480v1_genomic.fna/checkm_input GCF_014634805.1_ASM1463480v1_genomic.fna/checkm_result
[2024-01-24 11:06:02,525] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:02,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:02,546] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:02,547] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:02,547] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014634805.1_ASM1463480v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:02,548] [INFO] Task started: Blastn
[2024-01-24 11:06:02,548] [INFO] Running command: blastn -query GCF_014634805.1_ASM1463480v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20db37fe-baf0-42fb-91d6-352366548dc7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014634805.1_ASM1463480v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:03,405] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:03,408] [INFO] Selected 18 target genomes.
[2024-01-24 11:06:03,408] [INFO] Target genome list was writen to GCF_014634805.1_ASM1463480v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:03,423] [INFO] Task started: fastANI
[2024-01-24 11:06:03,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg483030e0-8d91-4612-80d5-917563f59259/GCF_014634805.1_ASM1463480v1_genomic.fna.gz --refList GCF_014634805.1_ASM1463480v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014634805.1_ASM1463480v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:11,225] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:11,238] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:11,238] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014634805.1	s__Leuconostoc falkenbergense	100.0	604	607	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.11	96.75	0.91	0.87	34	conclusive
GCF_014634745.1	s__Leuconostoc pseudomesenteroides	92.4614	522	607	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.98	96.85	0.90	0.84	11	-
GCF_000014445.1	s__Leuconostoc mesenteroides	80.7991	217	607	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.82	97.34	0.92	0.82	89	-
GCF_009676745.1	s__Leuconostoc mesenteroides_B	80.5202	213	607	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001891125.1	s__Leuconostoc suionicum	80.4292	229	607	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.16	97.05	0.94	0.91	7	-
GCF_008107645.1	s__Leuconostoc litchii	79.9644	199	607	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000166735.2	s__Leuconostoc inhae	79.8634	138	607	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.95	98.13	0.88	0.76	13	-
GCF_000092505.1	s__Leuconostoc kimchii	79.8534	195	607	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.55	99.53	0.95	0.95	3	-
GCF_000166715.1	s__Leuconostoc gelidum	79.6074	147	607	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.91	98.75	0.91	0.89	3	-
GCF_014207505.1	s__Leuconostoc carnosum	79.6031	148	607	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.31	98.70	0.92	0.87	17	-
GCF_012396485.1	s__Leuconostoc holzapfelii	79.539	148	607	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908715.1	s__Leuconostoc rapi	79.2278	158	607	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:11,240] [INFO] GTDB search result was written to GCF_014634805.1_ASM1463480v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:11,241] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:11,245] [INFO] DFAST_QC result json was written to GCF_014634805.1_ASM1463480v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:11,245] [INFO] DFAST_QC completed!
[2024-01-24 11:06:11,245] [INFO] Total running time: 0h0m43s